The Impact of Probiotics on Antibiotic Resistance in Soil Microbiomes
Implications for Sustainable Agriculture
Soil health gets shaped by a tangle of forces, but the bacteria clustered around plant roots play a starring role. Probiotics—yeah, the same ones hyped for gut health in people and animals—are now popping up as tools for soil management, supposedly boosting plant growth and nudging the microbial community into balance. Recent studies suggest that probiotics in soil can also influence the transfer of antibiotic resistance genes between bacteria.
People are paying more attention to the impact of probiotics on antibiotic resistance in soil, mostly because soils already carry a substantial load of resistance genes, thanks in part to years of agricultural use of antibiotics. Probiotics may help steer the soil microbiome in a beneficial direction, but they can also introduce or transfer resistance genes. That can ripple out, affecting not just soil and plants, but also food safety and, honestly, human health when resistant bacteria make their way up the food chain.
Key Takeaways
Probiotics can shake up antibiotic resistance gene patterns in soil.
What happens in the soil can have a profound impact on both plant and public health.
Ongoing research is shaping smarter, safer ways to use probiotics in agriculture.
Overview of Antibiotic Resistance in Soil Microbiomes
Antibiotic resistance in soil continues to raise concerns, primarily due to its impact on soil health and the significant risk it poses to humans. Soil microbiomes act as deep gene banks, full of resistance genes—some ancient, some new, shaped by both nature and human habits.
Antibiotic Resistome and Its Environmental Significance
The antibiotic resistome encompasses all the genes in soil microbes that enable them to resist antibiotics. You’ll find resistance genes not just in pathogens, but also in native soil bacteria. Natural microbial evolution and our agricultural practices both shape this pool of genes.
Soil retains resistance genes, both those that have been present for a long time and those that are relatively new arrivals. These genes don’t just sit there—they can jump to bacteria that infect people or animals. Things like heavy metals, fertilizers, and pollution can all nudge the resistome in new directions. Even low levels of antibiotics in the soil can prompt microbes to exchange resistance genes more frequently.
When the environment is loaded with resistance genes, the odds increase for antimicrobial resistance to emerge in pathogens that matter to us. Studies continue to show that soils exposed to antibiotics or waste contain more resistance genes. Sometimes, soil microbes pass these genes to bacteria that can cause disease in people or animals. There’s a solid review on the soil resistome if you want a deep dive. (Nesme & Simonet, 2015)
Mechanisms of Resistance: Intrinsic and Acquired
Soil microbes defend themselves in two significant ways: intrinsic resistance and acquired resistance. Innate resistance is built into their DNA, featuring characteristics such as rigid cell walls or enzymes that break down toxins.
Acquired resistance occurs when bacteria acquire new genes from their neighbors, typically through mobile genetic elements such as plasmids or transposons. This horizontal gene transfer enables soil bacteria to resist antibiotics they’ve never encountered before.
Using treated wastewater for irrigation or spreading animal manure can increase the prevalence of resistance genes in soil. Over time, these practices provide resistant bacteria with more opportunities to multiply and spread throughout the ecosystem.
Prevalence of Antibiotic Resistance Genes in Soil Ecosystems
Antibiotic resistance genes turn up in soils all over the world—untouched forests, sure, but especially where humans have been busy. Primeval forests retain many natural resistance genes as part of their stable microbiomes. But agricultural and urban soils? They’re often loaded with even more resistance genes.
Irrigating with treated wastewater or using manure as fertilizer tends to crank up resistance genes in farm soils. Those soils typically harbor bacteria with a diverse array of antimicrobial resistance features, and some of these genes can be transferred to microbes that cause harm to people.
Pollutants, antibiotics, and animal waste can turn soils into hotspots for the exchange of resistance genes. High microbial diversity provides bacteria with more opportunities to exchange and acquire new traits. For more on how antibiotics spread in soil microbiomes, check out this article on the impact of treated wastewater irrigation on antibiotic resistance. (Gatica & Cytryn, 2013)
Role of Probiotics in Soil Health Management
Probiotics play a surprisingly significant role in enhancing soil quality and maintaining a stable soil microbiome. These helpful microbes enhance nutrient cycling, suppress soil-borne pathogens, and generally make life easier for plants.
Types and Functions of Probiotic Microorganisms
Probiotic microorganisms in soil primarily comprise beneficial bacteria and certain fungi. Some notable species include lactic acid bacteria, such as Lactobacillus plantarum, which can improve soil structure and increase the availability of essential nutrients. Bacillus and Pseudomonas species also make significant contributions.
These microbes break down organic matter, fix nitrogen, and even tackle some pollutants. They help plants absorb nutrients, and in a neat twist, some strains produce compounds that slow down harmful microbes while giving beneficial ones a competitive edge. That’s how you get a healthier soil microbiome. (Suman et al., 2022)
Application of Probiotics as Biological Additives
People add probiotics to soils directly or incorporate them into biological additives, such as compost teas or biofertilizers. The blend you choose can be tailored to the specific crop or the soil's needs. Or it can be a blend of multiple species and nutrients to assist the crops.
Soil-based probiotics help restore microbial diversity that is often compromised by intensive farming or the use of chemicals. Products containing Lactobacillus plantarum and similar species can enrich the rhizosphere, stimulate plant growth, and even enhance crop resistance to disease, improve soil quality, and provide probiotics. (Zhang et al., 2025) These types of probiotics are also known as biostimulants. If you continue applying them, you typically see improved soil structure and fertility over time.
Interactions with Indigenous Soil Microbiota
Adding probiotics to the soil yields a whole new set of interactions with the indigenous soil microbiota. Sometimes they work together, sometimes they compete—it all depends on the environment and who’s already living there.
Probiotic bacteria can outcompete harmful organisms, and some produce natural antibiotics or enzymes to maintain balance. However, whether these new blends persist depends mainly on how diverse and resilient the native soil microbes are, as well as the diversity of probiotics. (Hu et al., 2016) Selecting the right probiotics and using them wisely can help maintain balance and support overall healthy soil.
Influence of Probiotics on Antibiotic Resistance Dynamics
Probiotics can alter the circulation of antibiotic resistance genes in soil microbiomes. They interact with native microbes and mobile genetic elements, which can shift how resistance spreads.
Impact on Horizontal Gene Transfer Mechanisms
Horizontal gene transfer (HGT) is the primary mechanism by which antibiotic resistance genes are transferred between bacteria. When you add probiotics to soil, you’re introducing new bacteria, and they may bring their resistance genes. These can spread to other soil bacteria through transformation, transduction, or conjugation.
Mobile genetic elements, including plasmids and transposons, drive the majority of horizontal gene transfer (HGT). (Pray, 2008) Probiotics carrying these elements can pass genes to native microbes. Some research suggests that factors such as bacterial density, moisture, and nutrient levels increase the likelihood of gene transfer.
There’s some evidence that in certain conditions, probiotics may increase how often soil bacteria swap genes. These shifts can help resistance spread through the soil microbial community, especially when antibiotics or stressors are hanging around.
Interactions with Antibiotic-Resistant Bacteria
Probiotics can affect the growth and survival of antibiotic-resistant bacteria in soil. Sometimes they crowd out resistant strains or slow them down by making acids or bacteriocins.
But here’s the catch: probiotics can also get cozy with antibiotic-resistant bacteria and even act as reservoirs for resistance genes. These close encounters can lead to gene swaps between probiotic strains and native soil bacteria. For instance, if a probiotic has a resistance gene on a plasmid, it can hand it off to other bacteria.
When antibiotics or environmental stress are present, these exchanges occur more frequently. In such cases, probiotics may unintentionally facilitate the spread of resistance traits among soil microbes—see Antibiotic Resistance and Probiotics: Knowledge Gaps, Market Overview, and Preliminary Screenings for more information on this topic. (Zavišić et al., 2023)
Effects on Mobile Genetic Elements in Soil
Mobile genetic elements, such as plasmids, transposons, and integrons, play a significant role in the transmission of antibiotic resistance genes. When people add probiotics to soil, they often also include extra mobile genetic elements. Sometimes, these bits of DNA come packed with several resistance genes, which could increase the risk of multi-drug resistance genes spreading.
Lots of things affect how these genetic elements swap hands: the mix of microbes in the soil, how disturbed the ground gets, and what’s floating around in the environment. Soil that is churned up frequently or has a higher concentration of antibiotics tends to exhibit more gene traffic.
Some research suggests that adding probiotics can increase both the diversity and sheer number of mobile genetic elements in soil. That means there is a larger gene pool and potentially more opportunities for resistance genes to spread, as mentioned in mobile antimicrobial resistance genes in probiotics and the propagation of antibiotic resistance genes in soil-plant systems. (Toth et al., 2021; Shen et al., 2024)
Pathways of Antimicrobial Resistance Dissemination
Antimicrobial resistance (AMR) in soil can originate from various sources, each contributing its load of resistant bacteria and genes to the already complex web of soil microbes. Understanding how animal waste, urban farming, compost, and chemical contaminants all contribute to this issue is crucial for maintaining healthy soil and minimizing risk.
Transmission via Animal Manure and Treated Manure
Animal manure, especially from large livestock operations, is a significant contributor to antimicrobial resistance in the soil. When animals receive antibiotics, resistant bacteria and antimicrobial resistance genes (ARGs) accumulate in their gut. These end up in manure, which then spreads both antibiotics and resistance genes onto fields.
Treated manure—whether it’s composted or processed—can still hang onto antibiotic residues and resistant bacteria, especially if farms use a lot of veterinary drugs. Resistant bugs can spread out in the environment, sometimes swapping genes directly with human pathogens through horizontal gene transfer. Researchers have examined ARGs in manure as a significant driver of resistance in soil microbiomes. For more information, refer to the discussion on the propagation of antibiotic resistance through probiotics. (Daniali, 2020)
Urban Agriculture and Soil Amendments
Urban soils get a lot of amendments: compost, manure, biosolids—you name it—to boost fertility. In cities, these inputs can carry antimicrobial resistance genes from various sources, including both animal and human sources. Additionally, city farms are exposed to additional pollutants, which can interfere with how antibiotic resistance (AMR) spreads.
Using manure and compost repeatedly in urban gardens can load the soil with resistant bacteria, as those materials may already contain resistance genes. The close quarters of city farming mean resistance genes can more easily reach people. As reviewed in this article on pathogen control in the built environment, maintaining antimicrobial resistance (AMR) in check in urban areas is a significant concern for public health. (D’Accolti et al., 2022)
Influence of Composting Practices
People use composting to process manure and other organic waste before it reaches the soil. If managed well, composting knocks down the number of live pathogens and resistant bacteria. Still, not everything gets wiped out—some microbes and resistance genes stick around.
Composting’s success depends on factors such as temperature, the duration of the process, and the composition of the pile. If the process doesn’t finish, antibiotics and ARGs might survive and end up in the soil. Not all compost is equal: manure-based compost typically carries a higher risk of antimicrobial resistance (AMR) compared to plant-based compost. (Jadeja, 2022)
Role of Chemical Contaminants and Heavy Metals
Chemical contaminants, such as pesticides and leftover veterinary drugs, can shape resistance in soil. Heavy metals such as copper, zinc, and mercury are commonly found near farms and in urban soils. These metals encourage bacteria to retain resistance genes, as some resistance mechanisms are effective against both antibiotics and metals.
When heavy metals and antibiotics pile up together, they can boost the number of resistant bacteria, even if no one’s using many antibiotics. Studies on mobile antimicrobial resistance genes in probiotics highlight the significant role the environment plays in the transfer of these genes. (Toth et al., 2021) Therefore, monitoring chemical contamination is a crucial step in combating resistance in soil.
Interactions Between Soil and Plant-Associated Microbiomes
Soil and plant microbiomes are constantly talking—bacteria move between roots, leaves, and the dirt nearby. This back-and-forth process determines how resistance genes are transferred from soil into plants and, ultimately, into the food that people eat.
Microbiota Composition in Rhizosphere and Root
The rhizosphere—the soil hugging plant roots—is packed with bacteria, fungi, and other microbes. These organisms interact with roots, making tangled networks that help plants thrive. Roots leak out compounds that feed good bacteria, and those bacteria help plants suck up nutrients.
Key microbes in the rhizosphere? You’ll find plenty of Pseudomonas, Bacillus, and a bunch of others. What’s there depends on soil quality, moisture, and the type of plant. The root microbiome tends to be more stable than the rest of the soil, acting as a filter to select which microbes can colonize within root tissues.
Adding probiotics or other microbial products to soil can sometimes boost disease suppression. (Hu et al., 2016) Still, it’s not always straightforward—they might also disrupt the balance, which could alter how resistance genes are passed around.
The Phyllosphere and Vegetable Microbiomes
The phyllosphere—the surface of plant leaves—hosts its unique microbiome. Leafy greens like lettuce and kale have a different set of bacteria on top than what’s down near the roots or in the soil. The mix changes with the weather, plant type, and other factors at the farm.
Bacteria on leaves must cope with harsh conditions, including sunlight, dryness, and exposure to the air. Even so, a surprisingly wide variety of microbes inhabit these areas, and some carry resistance genes. On fresh produce, bacteria can come from both soil and water. These communities matter for leafy greens, since they affect plant health and the safety of what ends up on your plate.
Transfer of Resistance Genes to Fresh Produce
Resistance genes can hitch a ride from soil microbes to plant roots, then make their way into the edible parts of the plant. Most research indicates that resistance genes in greens, such as lettuce or kale, originate from bacteria in the rhizosphere soil or roots.
When plant and soil bacteria work together, they can make this transfer more likely. For instance, if plants grow in soil loaded with numerous resistance genes, those genes can be present in the parts people eat. (Shen et al., 2024) That’s especially sketchy for produce eaten raw, since it could let resistance genes slip from farm to fork.
To minimize risks, farmers must carefully consider the products they use for fertilizer, irrigation, and microbial applications. Watching both the soil and plant microbes helps manage the transfer of resistance genes into food crops. (Roca et al., 2024)
Implications for Food Safety and Public Health
Soil microbiomes can shape the safety of food and public health. Using probiotics in soil may alter how antibiotic resistance and harmful bacteria spread through the environment, sometimes for the better, sometimes not. (Roca et al., 2024)
Risk of Food-Borne Illness and Human Pathogen Transmission
When people add probiotics to soil, they can change how bacteria act and interact. In some cases, this may reduce the risk of harmful bacteria, such as E. coli or Salmonella, reaching crops, which could lower the likelihood of people contracting foodborne illnesses.
However, if probiotics carry or acquire resistance genes, they may pass those on to pathogens in the soil. This gene swapping could help harmful microbes survive treatments that would usually eliminate them. There have been cases where antibiotic-resistant bacteria have been found on fresh produce, raising concerns about food safety and the need for improved management in agriculture.
Key concerns include:
Resistance genes moving from probiotics to pathogens
Human pathogens sticking around on or in crops
Risks for people eating the food, especially if their immune systems are weak
Antibiotic-Resistant Pathogens in the Food Chain
Antibiotic resistance in soil bacteria can spread up the food chain. (Kumar et al., 2020) If farm soil contains bacteria with resistance genes, those bacteria or their genes can transfer to crops, and then to whoever eats them—people or animals.
This can help spread antibiotic-resistant infections, making foodborne illness more challenging to treat. Health agencies worry about resistant E. coli or Salmonella that survive in soil and can be transmitted through produce, as these can cause serious trouble for people who become infected.
To fight back, people monitor soil health, test food, and adjust farming practices to reduce bacterial loads and prevent the transmission of resistance genes.
One Health Perspective on Soil and Human Health
The One Health approach states that the health of soil, food, and people is interconnected. Soil isn’t just dirt—it’s a hub for microbes, including those with antibiotic resistance.
If farmers use probiotics wisely, they may help maintain healthy soil microbiomes and reduce the risk of resistance. However, adding new bacteria to soil isn’t always predictable; it may have unintended side effects. It’s essential to monitor the impact of antimicrobial resistance on food safety and human health. (Ifedinezi et al., 2024)
Tackling antibiotic resistance in soils requires teamwork—doctors, veterinarians, farmers, and environmental professionals all need to collaborate. That’s how you get safer food and better public health, starting right at the soil.
Current Research Trends and Future Directions
Researchers are now employing advanced methods to track how probiotics affect soil resistance genes and overall microbial health. There is also considerable attention to how human activities, such as farming and urban expansion, alter soil microbiomes and present new challenges.
Metagenomic Approaches and Systems-Level Insights
Scientists utilize metagenomic techniques to examine all the genetic material present in soil samples. That allows them to identify genes associated with antibiotic resistance and observe shifts across the entire community, not just in a single species. It’s a real window into how the whole system changes.
With metagenomics, researchers can track how probiotics affect resistance gene levels over time and observe the transfer of resistance between species. These tools make it easier to determine whether adding probiotics will increase or decrease the risks.
More studies are calling for large, long-term projects to detect even small changes in these complex, ever-changing ecosystems. Sharing data across research groups is becoming the norm, which helps solidify findings.
Impacts of Climate Change and Urbanization
Rising temperatures and shifting rainfall patterns—thanks to climate change—are altering how microbes interact in soil. Some bacteria end up sharing resistance genes more readily. Urbanization alters land use, often reducing soil diversity and placing additional stress on microbial communities.
City soils tend to accumulate more antibiotics and heavy metals, both of which appear to exacerbate antibiotic resistance among microbes. As the climate continues to change, pathogens and beneficial microbes alike can migrate outside their usual zones, further exacerbating the chaos.
Trying to use probiotics in these unpredictable conditions? Sometimes it just doesn’t pan out. Scientists are still working to determine how these shifting environments affect whether probiotics can safely and effectively help control resistance.
Antibiotic Use in Agriculture and Regulatory Policies
Farmers often turn to antibiotics to boost animal growth and combat disease, but this practice contributes to soil resistance problems. Some folks are now looking at probiotics as a possible workaround, especially in organic farming, where you can’t just toss in any synthetic chemical you want.
Regulatory agencies have started drafting rules on both antibiotics and probiotics in agriculture. They’re setting limits, writing guidelines, and trying to keep track of how all this affects the soil’s microbiome. But let’s be honest—enforcement and monitoring still vary wildly from country to country.
Researchers and governments continue to test new policy ideas, aiming to encourage agriculture toward more sustainable practices. These policy papers consistently emphasize the need for agencies, scientists, and farmers to collaborate, particularly in addressing the global challenge of bacterial drug resistance. (Karnwal et al., 2025)
References
D’Accolti M, Soffritti I, Bini F, Mazziga E, Mazzacane S, Caselli E. Pathogen Control in the Built Environment: A Probiotic-Based System as a Remedy for the Spread of Antibiotic Resistance. Microorganisms. 2022; 10(2):225. https://doi.org/10.3390/microorganisms10020225
Daniali, M., Nikfar, S., & Abdollahi, M. (2020). Antibiotic resistance propagation through probiotics. Expert Opinion on Drug Metabolism & Toxicology, 16(12), 1207–1215. https://doi.org/10.1080/17425255.2020.1825682
Gatica, J., & Cytryn, E. (2013). Impact of treated wastewater irrigation on antibiotic resistance in the soil microbiome. Environmental Science and Pollution Research, 20, 3529-3538.
Hu, J., Wei, Z., Friman, V. P., Gu, S. H., Wang, X. F., Eisenhauer, N., ... & Jousset, A. (2016). Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression. MBio, 7(6), 10-1128.
Ifedinezi, O. V., Nnaji, N. D., Anumudu, C. K., Ekwueme, C. T., Uhegwu, C. C., Ihenetu, F. C., Obioha, P., Simon, B. O., Ezechukwu, P. S., & Onyeaka, H. (2024). Environmental Antimicrobial Resistance: Implications for Food Safety and Public Health. Antibiotics, 13(11), 1087. https://doi.org/10.3390/antibiotics13111087
Jadeja, N. B., & Worrich, A. (2022). From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches. Environmental Microbiology, 24(8), 3290-3306.
Karnwal, A., Jassim, A. Y., Mohammed, A. A., Mohammad Said, A. R., Selvaraj, M., & Malik, T. (2025). Addressing the global challenge of bacterial drug resistance: Insights, strategies, and future directions. Frontiers in Microbiology, 16, 1517772. https://doi.org/10.3389/fmicb.2025.1517772
Kumar, S. B., Arnipalli, S. R., & Ziouzenkova, O. (2020). Antibiotics in Food Chain: The Consequences for Antibiotic Resistance. Antibiotics, 9(10), 688. https://doi.org/10.3390/antibiotics9100688
Nesme, J., & Simonet, P. (2015). The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environmental microbiology, 17(4), 913-930.
Pray, L. (2008) Transposons: The jumping genes. Nature Education 1(1):204
Roca, A., Monge-Olivares, L., Matilla, M. A. (2024). Antibiotic-producing plant-associated bacteria, anti-virulence therapy and microbiome engineering: Integrated approaches in sustainable agriculture. https://doi.org/10.1111/1751-7915.70025 https://enviromicro-journals.onlinelibrary.wiley.com/doi/full/10.1111/1751-7915.70025
Shen, Y., Jiang, C., Zhang, B., Gao, H., Wang, X., & Guo, P. (2024). Dominant microbiome iteration and antibiotic resistance genes propagation way dictate the antibiotic resistance genes contamination degree in soil-plant system. Journal of Cleaner Production, 464, 142786. https://doi.org/10.1016/j.jclepro.2024.142786
Suman, J., Rakshit, A., Ogireddy, S. D., Singh, S., Gupta, C., & Chandrakala, J. (2022). Microbiome as a Key Player in Sustainable Agriculture and Human Health. Frontiers in Soil Science, 2, 821589. https://doi.org/10.3389/fsoil.2022.821589
Tóth AG, Csabai I, Judge MF, Maróti G, Becsei Á, Spisák S, Solymosi N. Mobile Antimicrobial Resistance Genes in Probiotics. Antibiotics. 2021; 10(11):1287. https://doi.org/10.3390/antibiotics10111287
Zavišić, G., Popović, M., Stojkov, S., Medić, D., Gusman, V., Lješković, N. J., & Galović, A. J. (2023). Antibiotic Resistance and Probiotics: Knowledge Gaps, Market Overview and Preliminary Screening. Antibiotics, 12(8), 1281. https://doi.org/10.3390/antibiotics12081281
Zhang, W., Wu, S., Jho, E. H., Chen, J., Liu, Q., Hu, J., Li, G., Zhao, X., & Sun, M. (2025). From soil to the intestinal tract: The key role of beneficial elements and probiotics in promoting health and longevity. Journal of Environmental Management, 384, 125611. https://doi.org/10.1016/j.jenvman.2025.125611